Starting phenix.real_space_refine on Sun Jun 29 10:06:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y82_39030/06_2025/8y82_39030_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y82_39030/06_2025/8y82_39030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y82_39030/06_2025/8y82_39030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y82_39030/06_2025/8y82_39030.map" model { file = "/net/cci-nas-00/data/ceres_data/8y82_39030/06_2025/8y82_39030_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y82_39030/06_2025/8y82_39030_neut_trim.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 166 5.49 5 Mg 4 5.21 5 S 124 5.16 5 C 21510 2.51 5 N 5934 2.21 5 O 6776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34514 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 3659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3659 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 443} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3629 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 27, 'TRANS': 428} Chain breaks: 2 Chain: "C" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "D" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "E" Number of atoms: 4609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4609 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 552} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3629 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 27, 'TRANS': 428} Chain breaks: 2 Chain: "G" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "H" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "I" Number of atoms: 3659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3659 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 443} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3629 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 27, 'TRANS': 428} Chain breaks: 2 Chain: "K" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "L" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "M" Number of atoms: 4609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4609 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 552} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3629 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 27, 'TRANS': 428} Chain breaks: 2 Chain: "O" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "P" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.77, per 1000 atoms: 0.63 Number of scatterers: 34514 At special positions: 0 Unit cell: (110.818, 151.341, 212.539, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 124 16.00 P 166 15.00 Mg 4 11.99 O 6776 8.00 N 5934 7.00 C 21510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.81 Conformation dependent library (CDL) restraints added in 4.0 seconds 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7320 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 50 sheets defined 42.1% alpha, 18.8% beta 60 base pairs and 104 stacking pairs defined. Time for finding SS restraints: 13.17 Creating SS restraints... Processing helix chain 'A' and resid 5 through 16 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.599A pdb=" N THR A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 176 Processing helix chain 'A' and resid 207 through 219 removed outlier: 4.111A pdb=" N CYS A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 242 removed outlier: 3.763A pdb=" N ASP A 242 " --> pdb=" O ARG A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 276 removed outlier: 3.784A pdb=" N GLN A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 383 through 391 Processing helix chain 'A' and resid 406 through 414 Processing helix chain 'A' and resid 414 through 430 Processing helix chain 'A' and resid 458 through 466 Processing helix chain 'A' and resid 513 through 519 removed outlier: 3.883A pdb=" N ARG A 517 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLU A 518 " --> pdb=" O ASP A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 529 Processing helix chain 'A' and resid 532 through 549 Processing helix chain 'B' and resid 21 through 25 Processing helix chain 'B' and resid 29 through 37 Processing helix chain 'B' and resid 39 through 43 removed outlier: 3.900A pdb=" N CYS B 43 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 60 through 72 removed outlier: 3.703A pdb=" N LEU B 64 " --> pdb=" O HIS B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 111 through 120 removed outlier: 3.646A pdb=" N GLY B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 118 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 134 Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 151 through 157 removed outlier: 4.515A pdb=" N LYS B 156 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 192 through 209 removed outlier: 3.788A pdb=" N VAL B 196 " --> pdb=" O CYS B 192 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 295 removed outlier: 3.607A pdb=" N SER B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 322 removed outlier: 3.528A pdb=" N GLN B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 429 removed outlier: 4.437A pdb=" N THR B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 459 Processing helix chain 'B' and resid 469 through 473 Processing helix chain 'E' and resid 5 through 16 Processing helix chain 'E' and resid 27 through 33 removed outlier: 3.508A pdb=" N ARG E 30 " --> pdb=" O GLY E 27 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY E 33 " --> pdb=" O ARG E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 53 Processing helix chain 'E' and resid 64 through 78 Processing helix chain 'E' and resid 88 through 98 Processing helix chain 'E' and resid 100 through 112 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'E' and resid 145 through 155 Processing helix chain 'E' and resid 168 through 176 removed outlier: 3.505A pdb=" N SER E 172 " --> pdb=" O TYR E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 203 removed outlier: 3.787A pdb=" N GLN E 202 " --> pdb=" O PRO E 199 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR E 203 " --> pdb=" O ASP E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 219 removed outlier: 3.910A pdb=" N ILE E 217 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG E 218 " --> pdb=" O ALA E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 242 Processing helix chain 'E' and resid 262 through 275 removed outlier: 3.651A pdb=" N GLN E 266 " --> pdb=" O GLU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 297 Processing helix chain 'E' and resid 302 through 310 removed outlier: 4.130A pdb=" N LYS E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 367 Processing helix chain 'E' and resid 383 through 391 removed outlier: 3.597A pdb=" N ILE E 387 " --> pdb=" O GLY E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 414 Processing helix chain 'E' and resid 414 through 430 Processing helix chain 'E' and resid 455 through 457 No H-bonds generated for 'chain 'E' and resid 455 through 457' Processing helix chain 'E' and resid 458 through 466 Processing helix chain 'E' and resid 517 through 519 No H-bonds generated for 'chain 'E' and resid 517 through 519' Processing helix chain 'E' and resid 520 through 529 Processing helix chain 'E' and resid 532 through 549 Processing helix chain 'F' and resid 21 through 25 Processing helix chain 'F' and resid 29 through 37 Processing helix chain 'F' and resid 39 through 44 Processing helix chain 'F' and resid 57 through 59 No H-bonds generated for 'chain 'F' and resid 57 through 59' Processing helix chain 'F' and resid 60 through 73 removed outlier: 3.727A pdb=" N LEU F 64 " --> pdb=" O HIS F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 95 Processing helix chain 'F' and resid 111 through 120 removed outlier: 3.563A pdb=" N GLY F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 132 Processing helix chain 'F' and resid 133 through 138 Processing helix chain 'F' and resid 151 through 157 removed outlier: 4.597A pdb=" N LYS F 156 " --> pdb=" O SER F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 174 Processing helix chain 'F' and resid 185 through 190 Processing helix chain 'F' and resid 193 through 208 Processing helix chain 'F' and resid 276 through 295 Processing helix chain 'F' and resid 312 through 323 removed outlier: 3.726A pdb=" N PHE F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 429 removed outlier: 4.073A pdb=" N THR F 421 " --> pdb=" O GLY F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 443 through 459 Processing helix chain 'F' and resid 469 through 473 Processing helix chain 'I' and resid 5 through 16 Processing helix chain 'I' and resid 121 through 132 Processing helix chain 'I' and resid 145 through 156 removed outlier: 3.599A pdb=" N THR I 149 " --> pdb=" O ASP I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 176 Processing helix chain 'I' and resid 207 through 219 removed outlier: 4.133A pdb=" N CYS I 211 " --> pdb=" O GLU I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 242 Processing helix chain 'I' and resid 262 through 275 removed outlier: 3.809A pdb=" N GLN I 266 " --> pdb=" O GLU I 262 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 296 Processing helix chain 'I' and resid 302 through 310 Processing helix chain 'I' and resid 355 through 367 Processing helix chain 'I' and resid 383 through 391 Processing helix chain 'I' and resid 406 through 414 Processing helix chain 'I' and resid 414 through 430 Processing helix chain 'I' and resid 458 through 466 Processing helix chain 'I' and resid 513 through 519 removed outlier: 3.883A pdb=" N ARG I 517 " --> pdb=" O LEU I 514 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLU I 518 " --> pdb=" O ASP I 515 " (cutoff:3.500A) Processing helix chain 'I' and resid 520 through 529 Processing helix chain 'I' and resid 532 through 549 Processing helix chain 'J' and resid 21 through 25 Processing helix chain 'J' and resid 29 through 37 Processing helix chain 'J' and resid 39 through 43 removed outlier: 3.889A pdb=" N CYS J 43 " --> pdb=" O TYR J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 59 No H-bonds generated for 'chain 'J' and resid 57 through 59' Processing helix chain 'J' and resid 60 through 72 removed outlier: 3.704A pdb=" N LEU J 64 " --> pdb=" O HIS J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 94 Processing helix chain 'J' and resid 111 through 120 removed outlier: 3.647A pdb=" N GLY J 115 " --> pdb=" O ASP J 111 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA J 118 " --> pdb=" O HIS J 114 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN J 119 " --> pdb=" O GLY J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 134 Processing helix chain 'J' and resid 135 through 137 No H-bonds generated for 'chain 'J' and resid 135 through 137' Processing helix chain 'J' and resid 151 through 157 removed outlier: 4.515A pdb=" N LYS J 156 " --> pdb=" O SER J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 174 Processing helix chain 'J' and resid 175 through 177 No H-bonds generated for 'chain 'J' and resid 175 through 177' Processing helix chain 'J' and resid 186 through 189 Processing helix chain 'J' and resid 192 through 209 removed outlier: 3.789A pdb=" N VAL J 196 " --> pdb=" O CYS J 192 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY J 209 " --> pdb=" O TYR J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 295 removed outlier: 3.608A pdb=" N SER J 294 " --> pdb=" O LEU J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 312 through 322 removed outlier: 3.529A pdb=" N GLN J 317 " --> pdb=" O GLU J 313 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER J 322 " --> pdb=" O GLY J 318 " (cutoff:3.500A) Processing helix chain 'J' and resid 417 through 429 removed outlier: 4.438A pdb=" N THR J 421 " --> pdb=" O GLY J 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 443 through 459 Processing helix chain 'J' and resid 469 through 473 Processing helix chain 'M' and resid 5 through 16 Processing helix chain 'M' and resid 27 through 31 Processing helix chain 'M' and resid 36 through 53 Processing helix chain 'M' and resid 64 through 78 Processing helix chain 'M' and resid 88 through 98 Processing helix chain 'M' and resid 100 through 112 Processing helix chain 'M' and resid 120 through 132 Processing helix chain 'M' and resid 145 through 155 removed outlier: 3.651A pdb=" N ALA M 150 " --> pdb=" O VAL M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 176 Processing helix chain 'M' and resid 198 through 203 removed outlier: 3.787A pdb=" N GLN M 202 " --> pdb=" O PRO M 199 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR M 203 " --> pdb=" O ASP M 200 " (cutoff:3.500A) Processing helix chain 'M' and resid 205 through 219 removed outlier: 3.598A pdb=" N ILE M 217 " --> pdb=" O LEU M 213 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG M 218 " --> pdb=" O ALA M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 230 through 242 Processing helix chain 'M' and resid 262 through 275 removed outlier: 3.652A pdb=" N GLN M 266 " --> pdb=" O GLU M 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 286 through 297 Processing helix chain 'M' and resid 302 through 310 removed outlier: 4.130A pdb=" N LYS M 308 " --> pdb=" O ALA M 304 " (cutoff:3.500A) Processing helix chain 'M' and resid 355 through 367 Processing helix chain 'M' and resid 383 through 391 removed outlier: 3.597A pdb=" N ILE M 387 " --> pdb=" O GLY M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 406 through 414 Processing helix chain 'M' and resid 414 through 430 Processing helix chain 'M' and resid 455 through 457 No H-bonds generated for 'chain 'M' and resid 455 through 457' Processing helix chain 'M' and resid 458 through 466 Processing helix chain 'M' and resid 517 through 519 No H-bonds generated for 'chain 'M' and resid 517 through 519' Processing helix chain 'M' and resid 520 through 529 Processing helix chain 'M' and resid 532 through 549 Processing helix chain 'N' and resid 21 through 25 Processing helix chain 'N' and resid 29 through 37 Processing helix chain 'N' and resid 39 through 44 Processing helix chain 'N' and resid 57 through 59 No H-bonds generated for 'chain 'N' and resid 57 through 59' Processing helix chain 'N' and resid 60 through 73 removed outlier: 3.727A pdb=" N LEU N 64 " --> pdb=" O HIS N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 95 Processing helix chain 'N' and resid 111 through 120 removed outlier: 3.563A pdb=" N GLY N 115 " --> pdb=" O ASP N 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 132 Processing helix chain 'N' and resid 133 through 138 Processing helix chain 'N' and resid 151 through 157 removed outlier: 4.596A pdb=" N LYS N 156 " --> pdb=" O SER N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 174 Processing helix chain 'N' and resid 184 through 190 removed outlier: 4.194A pdb=" N LEU N 188 " --> pdb=" O ASN N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 192 through 208 removed outlier: 3.563A pdb=" N VAL N 196 " --> pdb=" O CYS N 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 276 through 295 Processing helix chain 'N' and resid 312 through 323 removed outlier: 3.726A pdb=" N PHE N 323 " --> pdb=" O ALA N 319 " (cutoff:3.500A) Processing helix chain 'N' and resid 417 through 429 removed outlier: 4.074A pdb=" N THR N 421 " --> pdb=" O GLY N 417 " (cutoff:3.500A) Processing helix chain 'N' and resid 443 through 459 Processing helix chain 'N' and resid 469 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 137 through 140 Processing sheet with id=AA2, first strand: chain 'A' and resid 221 through 224 removed outlier: 6.098A pdb=" N LEU A 251 " --> pdb=" O TYR A 280 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL A 282 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TRP A 253 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 579 through 580 Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 338 removed outlier: 4.528A pdb=" N LEU A 501 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N HIS A 444 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 335 through 338 removed outlier: 4.528A pdb=" N LEU A 501 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 373 removed outlier: 6.899A pdb=" N ILE A 343 " --> pdb=" O TYR A 403 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TYR A 403 " --> pdb=" O ILE A 343 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N CYS A 345 " --> pdb=" O GLN A 401 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLN A 401 " --> pdb=" O CYS A 345 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 347 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE A 399 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR A 349 " --> pdb=" O ASN A 397 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 558 through 561 removed outlier: 3.528A pdb=" N ALA A 569 " --> pdb=" O CYS A 561 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 12 through 13 removed outlier: 6.812A pdb=" N GLU B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 19 through 20 Processing sheet with id=AB1, first strand: chain 'B' and resid 98 through 99 removed outlier: 7.113A pdb=" N VAL B 50 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N CYS B 107 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TYR B 54 " --> pdb=" O CYS B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 98 through 99 removed outlier: 7.113A pdb=" N VAL B 50 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE B 183 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL B 148 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AB4, first strand: chain 'E' and resid 138 through 139 removed outlier: 8.041A pdb=" N PHE E 139 " --> pdb=" O MET E 20 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TRP E 22 " --> pdb=" O PHE E 139 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N MET E 21 " --> pdb=" O VAL E 222 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N SER E 224 " --> pdb=" O MET E 21 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N PHE E 23 " --> pdb=" O SER E 224 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU E 221 " --> pdb=" O TYR E 252 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N THR E 254 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL E 223 " --> pdb=" O THR E 254 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N TRP E 253 " --> pdb=" O VAL E 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 161 through 162 Processing sheet with id=AB6, first strand: chain 'E' and resid 330 through 332 removed outlier: 3.910A pdb=" N LEU E 331 " --> pdb=" O SER E 580 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER E 580 " --> pdb=" O LEU E 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 335 through 338 removed outlier: 4.631A pdb=" N LEU E 501 " --> pdb=" O VAL E 338 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N HIS E 444 " --> pdb=" O ILE E 492 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 335 through 338 removed outlier: 4.631A pdb=" N LEU E 501 " --> pdb=" O VAL E 338 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 371 through 373 removed outlier: 6.625A pdb=" N ILE E 343 " --> pdb=" O TYR E 403 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TYR E 403 " --> pdb=" O ILE E 343 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N CYS E 345 " --> pdb=" O GLN E 401 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLN E 401 " --> pdb=" O CYS E 345 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL E 347 " --> pdb=" O ILE E 399 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE E 399 " --> pdb=" O VAL E 347 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR E 349 " --> pdb=" O ASN E 397 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 558 through 561 removed outlier: 3.615A pdb=" N ALA E 569 " --> pdb=" O CYS E 561 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 12 through 13 removed outlier: 3.989A pdb=" N SER F 12 " --> pdb=" O TYR F 366 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR F 366 " --> pdb=" O SER F 12 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU F 375 " --> pdb=" O PRO F 368 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU F 331 " --> pdb=" O PHE F 412 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE F 303 " --> pdb=" O GLU F 330 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL F 332 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ILE F 305 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE F 334 " --> pdb=" O ILE F 305 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LYS F 307 " --> pdb=" O ILE F 334 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 19 through 20 Processing sheet with id=AC4, first strand: chain 'F' and resid 98 through 99 removed outlier: 6.602A pdb=" N VAL F 50 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N CYS F 107 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR F 54 " --> pdb=" O CYS F 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 98 through 99 removed outlier: 6.602A pdb=" N VAL F 50 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG F 51 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU F 147 " --> pdb=" O ARG F 51 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA F 53 " --> pdb=" O LEU F 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 159 through 160 removed outlier: 3.927A pdb=" N TYR F 160 " --> pdb=" O PHE F 163 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 381 through 382 Processing sheet with id=AC8, first strand: chain 'I' and resid 137 through 140 Processing sheet with id=AC9, first strand: chain 'I' and resid 221 through 224 removed outlier: 6.098A pdb=" N LEU I 251 " --> pdb=" O TYR I 280 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL I 282 " --> pdb=" O LEU I 251 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TRP I 253 " --> pdb=" O VAL I 282 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 579 through 580 Processing sheet with id=AD2, first strand: chain 'I' and resid 335 through 338 removed outlier: 4.529A pdb=" N LEU I 501 " --> pdb=" O VAL I 338 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N HIS I 444 " --> pdb=" O ILE I 492 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 335 through 338 removed outlier: 4.529A pdb=" N LEU I 501 " --> pdb=" O VAL I 338 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 371 through 373 removed outlier: 6.899A pdb=" N ILE I 343 " --> pdb=" O TYR I 403 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TYR I 403 " --> pdb=" O ILE I 343 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N CYS I 345 " --> pdb=" O GLN I 401 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLN I 401 " --> pdb=" O CYS I 345 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL I 347 " --> pdb=" O ILE I 399 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE I 399 " --> pdb=" O VAL I 347 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR I 349 " --> pdb=" O ASN I 397 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 558 through 561 removed outlier: 3.528A pdb=" N ALA I 569 " --> pdb=" O CYS I 561 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 12 through 13 removed outlier: 6.812A pdb=" N GLU J 373 " --> pdb=" O LEU J 369 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA J 223 " --> pdb=" O LYS J 302 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 19 through 20 Processing sheet with id=AD8, first strand: chain 'J' and resid 98 through 99 removed outlier: 7.114A pdb=" N VAL J 50 " --> pdb=" O VAL J 99 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N CYS J 107 " --> pdb=" O LEU J 52 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TYR J 54 " --> pdb=" O CYS J 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'J' and resid 98 through 99 removed outlier: 7.114A pdb=" N VAL J 50 " --> pdb=" O VAL J 99 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE J 183 " --> pdb=" O LEU J 146 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL J 148 " --> pdb=" O ILE J 183 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AE2, first strand: chain 'M' and resid 138 through 140 removed outlier: 8.041A pdb=" N PHE M 139 " --> pdb=" O MET M 20 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TRP M 22 " --> pdb=" O PHE M 139 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N MET M 21 " --> pdb=" O VAL M 222 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N SER M 224 " --> pdb=" O MET M 21 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N PHE M 23 " --> pdb=" O SER M 224 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU M 221 " --> pdb=" O TYR M 252 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N THR M 254 " --> pdb=" O LEU M 221 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL M 223 " --> pdb=" O THR M 254 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N TRP M 253 " --> pdb=" O VAL M 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'M' and resid 161 through 162 Processing sheet with id=AE4, first strand: chain 'M' and resid 330 through 332 removed outlier: 3.910A pdb=" N LEU M 331 " --> pdb=" O SER M 580 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER M 580 " --> pdb=" O LEU M 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'M' and resid 335 through 338 removed outlier: 4.631A pdb=" N LEU M 501 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS M 444 " --> pdb=" O ILE M 492 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 335 through 338 removed outlier: 4.631A pdb=" N LEU M 501 " --> pdb=" O VAL M 338 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 371 through 373 removed outlier: 6.625A pdb=" N ILE M 343 " --> pdb=" O TYR M 403 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TYR M 403 " --> pdb=" O ILE M 343 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N CYS M 345 " --> pdb=" O GLN M 401 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLN M 401 " --> pdb=" O CYS M 345 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL M 347 " --> pdb=" O ILE M 399 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE M 399 " --> pdb=" O VAL M 347 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR M 349 " --> pdb=" O ASN M 397 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 558 through 561 removed outlier: 3.616A pdb=" N ALA M 569 " --> pdb=" O CYS M 561 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 12 through 13 removed outlier: 3.990A pdb=" N SER N 12 " --> pdb=" O TYR N 366 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR N 366 " --> pdb=" O SER N 12 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU N 375 " --> pdb=" O PRO N 368 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU N 331 " --> pdb=" O PHE N 412 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE N 303 " --> pdb=" O GLU N 330 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL N 332 " --> pdb=" O ILE N 303 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ILE N 305 " --> pdb=" O VAL N 332 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE N 334 " --> pdb=" O ILE N 305 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LYS N 307 " --> pdb=" O ILE N 334 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS N 244 " --> pdb=" O TYR N 260 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 19 through 20 Processing sheet with id=AF2, first strand: chain 'N' and resid 98 through 99 removed outlier: 6.602A pdb=" N VAL N 50 " --> pdb=" O VAL N 99 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N CYS N 107 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR N 54 " --> pdb=" O CYS N 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'N' and resid 98 through 99 removed outlier: 6.602A pdb=" N VAL N 50 " --> pdb=" O VAL N 99 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ARG N 51 " --> pdb=" O VAL N 145 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU N 147 " --> pdb=" O ARG N 51 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA N 53 " --> pdb=" O LEU N 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'N' and resid 159 through 160 removed outlier: 3.927A pdb=" N TYR N 160 " --> pdb=" O PHE N 163 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 381 through 382 1385 hydrogen bonds defined for protein. 3870 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 144 hydrogen bonds 272 hydrogen bond angles 0 basepair planarities 60 basepair parallelities 104 stacking parallelities Total time for adding SS restraints: 15.03 Time building geometry restraints manager: 10.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5309 1.32 - 1.44: 10697 1.44 - 1.57: 19148 1.57 - 1.69: 324 1.69 - 1.82: 190 Bond restraints: 35668 Sorted by residual: bond pdb=" N PHE I 247 " pdb=" CA PHE I 247 " ideal model delta sigma weight residual 1.458 1.485 -0.028 7.40e-03 1.83e+04 1.39e+01 bond pdb=" CA SER M 167 " pdb=" CB SER M 167 " ideal model delta sigma weight residual 1.541 1.503 0.038 1.20e-02 6.94e+03 1.00e+01 bond pdb=" C PRO M 35 " pdb=" O PRO M 35 " ideal model delta sigma weight residual 1.233 1.199 0.035 1.10e-02 8.26e+03 9.91e+00 bond pdb=" C THR N 189 " pdb=" O THR N 189 " ideal model delta sigma weight residual 1.236 1.195 0.041 1.32e-02 5.74e+03 9.75e+00 bond pdb=" N THR J 401 " pdb=" CA THR J 401 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.04e-02 9.25e+03 9.45e+00 ... (remaining 35663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 48026 2.27 - 4.54: 921 4.54 - 6.81: 104 6.81 - 9.09: 20 9.09 - 11.36: 9 Bond angle restraints: 49080 Sorted by residual: angle pdb=" N GLN N 191 " pdb=" CA GLN N 191 " pdb=" C GLN N 191 " ideal model delta sigma weight residual 110.80 122.16 -11.36 2.13e+00 2.20e-01 2.84e+01 angle pdb=" N ILE N 462 " pdb=" CA ILE N 462 " pdb=" C ILE N 462 " ideal model delta sigma weight residual 113.20 108.09 5.11 9.60e-01 1.09e+00 2.83e+01 angle pdb=" N ILE F 462 " pdb=" CA ILE F 462 " pdb=" C ILE F 462 " ideal model delta sigma weight residual 113.20 108.11 5.09 9.60e-01 1.09e+00 2.81e+01 angle pdb=" C GLN I 15 " pdb=" N ASN I 16 " pdb=" CA ASN I 16 " ideal model delta sigma weight residual 123.03 116.09 6.94 1.34e+00 5.57e-01 2.69e+01 angle pdb=" N LEU M 14 " pdb=" CA LEU M 14 " pdb=" C LEU M 14 " ideal model delta sigma weight residual 111.28 105.67 5.61 1.09e+00 8.42e-01 2.65e+01 ... (remaining 49075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 19914 35.84 - 71.68: 1210 71.68 - 107.52: 63 107.52 - 143.36: 0 143.36 - 179.20: 9 Dihedral angle restraints: 21196 sinusoidal: 9828 harmonic: 11368 Sorted by residual: dihedral pdb=" C5' AMP E 601 " pdb=" O5' AMP E 601 " pdb=" P AMP E 601 " pdb=" O3P AMP E 601 " ideal model delta sinusoidal sigma weight residual -60.00 119.20 -179.20 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" N SER E 167 " pdb=" C SER E 167 " pdb=" CA SER E 167 " pdb=" CB SER E 167 " ideal model delta harmonic sigma weight residual 122.80 133.95 -11.15 0 2.50e+00 1.60e-01 1.99e+01 dihedral pdb=" C2' AMP M 601 " pdb=" C1' AMP M 601 " pdb=" N9 AMP M 601 " pdb=" C4 AMP M 601 " ideal model delta sinusoidal sigma weight residual 91.55 168.06 -76.50 1 2.00e+01 2.50e-03 1.84e+01 ... (remaining 21193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 5178 0.095 - 0.190: 281 0.190 - 0.284: 19 0.284 - 0.379: 5 0.379 - 0.474: 3 Chirality restraints: 5486 Sorted by residual: chirality pdb=" CA ALA N 187 " pdb=" N ALA N 187 " pdb=" C ALA N 187 " pdb=" CB ALA N 187 " both_signs ideal model delta sigma weight residual False 2.48 2.01 0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" CA SER E 167 " pdb=" N SER E 167 " pdb=" C SER E 167 " pdb=" CB SER E 167 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" CA ARG J 190 " pdb=" N ARG J 190 " pdb=" C ARG J 190 " pdb=" CB ARG J 190 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.46 2.00e-01 2.50e+01 5.18e+00 ... (remaining 5483 not shown) Planarity restraints: 5684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU I 14 " -0.020 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C LEU I 14 " 0.072 2.00e-02 2.50e+03 pdb=" O LEU I 14 " -0.027 2.00e-02 2.50e+03 pdb=" N GLN I 15 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER M 31 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C SER M 31 " -0.059 2.00e-02 2.50e+03 pdb=" O SER M 31 " 0.022 2.00e-02 2.50e+03 pdb=" N ALA M 32 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS I 315 " 0.051 5.00e-02 4.00e+02 7.45e-02 8.88e+00 pdb=" N PRO I 316 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO I 316 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO I 316 " 0.041 5.00e-02 4.00e+02 ... (remaining 5681 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 45 2.20 - 2.88: 13477 2.88 - 3.55: 50725 3.55 - 4.23: 85171 4.23 - 4.90: 144233 Nonbonded interactions: 293651 Sorted by model distance: nonbonded pdb=" OH TYR E 168 " pdb=" CB GLN M 192 " model vdw 1.526 3.440 nonbonded pdb=" OE1 GLU J 330 " pdb=" CA GLY J 414 " model vdw 1.815 3.440 nonbonded pdb=" OD2 ASP F 261 " pdb=" CG1 VAL F 463 " model vdw 1.885 3.460 nonbonded pdb=" CB GLN E 192 " pdb=" OH TYR M 168 " model vdw 1.898 3.440 nonbonded pdb=" OD2 ASP E 188 " pdb=" NH1 ARG E 190 " model vdw 1.909 3.120 ... (remaining 293646 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 5 through 473) selection = chain 'J' selection = (chain 'N' and resid 5 through 473) } ncs_group { reference = (chain 'C' and resid 1 through 21) selection = chain 'G' selection = (chain 'K' and resid 1 through 21) selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.480 Check model and map are aligned: 0.260 Set scattering table: 0.320 Process input model: 88.480 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.410 35670 Z= 0.315 Angle : 0.714 11.358 49080 Z= 0.410 Chirality : 0.047 0.474 5486 Planarity : 0.005 0.076 5684 Dihedral : 20.404 179.197 13876 Min Nonbonded Distance : 1.526 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.63 % Favored : 95.21 % Rotamer: Outliers : 1.83 % Allowed : 30.62 % Favored : 67.56 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3842 helix: 0.73 (0.14), residues: 1476 sheet: -0.67 (0.20), residues: 758 loop : -0.64 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 502 HIS 0.011 0.001 HIS M 52 PHE 0.016 0.001 PHE M 287 TYR 0.019 0.001 TYR N 274 ARG 0.004 0.000 ARG B 411 Details of bonding type rmsd hydrogen bonds : bond 0.15270 ( 1469) hydrogen bonds : angle 6.39042 ( 4142) covalent geometry : bond 0.00388 (35668) covalent geometry : angle 0.71429 (49080) Misc. bond : bond 0.30703 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 761 time to evaluate : 3.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.7792 (mm) cc_final: 0.7539 (tt) REVERT: B 100 MET cc_start: 0.6540 (mmm) cc_final: 0.5933 (tpt) REVERT: E 93 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8169 (m-80) REVERT: I 15 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7772 (tt0) REVERT: J 302 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8315 (tttt) REVERT: M 30 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7573 (ttm170) REVERT: M 48 TYR cc_start: 0.6424 (t80) cc_final: 0.6074 (t80) REVERT: M 133 ASN cc_start: 0.7722 (t0) cc_final: 0.7072 (t0) REVERT: M 165 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7218 (mm-30) REVERT: M 198 THR cc_start: 0.7157 (m) cc_final: 0.6935 (m) REVERT: M 332 ARG cc_start: 0.7614 (ttp-170) cc_final: 0.7093 (ttt180) REVERT: M 461 LEU cc_start: 0.6202 (tp) cc_final: 0.5806 (mp) REVERT: M 546 ILE cc_start: 0.7237 (mt) cc_final: 0.6675 (mt) REVERT: M 566 GLU cc_start: 0.3991 (mp0) cc_final: 0.3251 (tt0) REVERT: M 579 PHE cc_start: 0.6685 (p90) cc_final: 0.6308 (p90) REVERT: N 40 TYR cc_start: 0.7166 (t80) cc_final: 0.6876 (t80) REVERT: N 70 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6512 (tt0) REVERT: N 276 SER cc_start: 0.8212 (p) cc_final: 0.8007 (m) REVERT: N 280 MET cc_start: 0.8263 (tpp) cc_final: 0.8053 (tpt) REVERT: N 376 LEU cc_start: 0.7331 (tp) cc_final: 0.7020 (tp) outliers start: 61 outliers final: 27 residues processed: 815 average time/residue: 0.5923 time to fit residues: 757.2000 Evaluate side-chains 521 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 489 time to evaluate : 3.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain I residue 266 GLN Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain I residue 326 LYS Chi-restraints excluded: chain I residue 329 PRO Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain J residue 190 ARG Chi-restraints excluded: chain J residue 302 LYS Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain M residue 189 PHE Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 211 CYS Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 270 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 339 optimal weight: 20.0000 chunk 304 optimal weight: 0.0980 chunk 169 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 205 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 315 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 234 optimal weight: 4.9990 chunk 365 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 HIS ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 HIS F 238 GLN ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN I 120 ASN I 123 HIS I 244 ASN J 60 HIS ** M 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 GLN ** M 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 186 HIS M 533 ASN ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 296 ASN ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 450 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.153203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.120919 restraints weight = 58223.963| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.66 r_work: 0.3482 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 35670 Z= 0.238 Angle : 0.697 9.358 49080 Z= 0.356 Chirality : 0.044 0.199 5486 Planarity : 0.005 0.047 5684 Dihedral : 18.039 171.696 6558 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 6.38 % Allowed : 27.86 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3842 helix: 0.77 (0.13), residues: 1466 sheet: -0.70 (0.19), residues: 784 loop : -0.75 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 543 HIS 0.017 0.001 HIS E 52 PHE 0.024 0.002 PHE N 21 TYR 0.024 0.002 TYR N 87 ARG 0.009 0.001 ARG B 411 Details of bonding type rmsd hydrogen bonds : bond 0.05294 ( 1469) hydrogen bonds : angle 5.14624 ( 4142) covalent geometry : bond 0.00544 (35668) covalent geometry : angle 0.69728 (49080) Misc. bond : bond 0.00660 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 509 time to evaluate : 3.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASN cc_start: 0.9000 (OUTLIER) cc_final: 0.8658 (p0) REVERT: A 21 MET cc_start: 0.7422 (ttm) cc_final: 0.7215 (ttm) REVERT: A 22 TRP cc_start: 0.8380 (m100) cc_final: 0.8040 (m100) REVERT: A 136 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7786 (mptp) REVERT: A 213 LEU cc_start: 0.8052 (mm) cc_final: 0.7650 (mm) REVERT: A 243 GLN cc_start: 0.6674 (OUTLIER) cc_final: 0.6459 (mp10) REVERT: A 289 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8403 (tm-30) REVERT: A 379 LEU cc_start: 0.7881 (mm) cc_final: 0.7668 (tt) REVERT: B 100 MET cc_start: 0.7091 (mmm) cc_final: 0.6554 (mmm) REVERT: E 93 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8316 (m-80) REVERT: E 132 MET cc_start: 0.8767 (ttp) cc_final: 0.8531 (ttt) REVERT: E 572 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7421 (pt0) REVERT: I 206 ARG cc_start: 0.5933 (tpt90) cc_final: 0.5539 (ptt-90) REVERT: I 463 LYS cc_start: 0.7979 (tppt) cc_final: 0.7696 (tppt) REVERT: I 537 TYR cc_start: 0.7745 (t80) cc_final: 0.7534 (t80) REVERT: I 547 LEU cc_start: 0.8138 (mm) cc_final: 0.7929 (mm) REVERT: J 40 TYR cc_start: 0.8659 (t80) cc_final: 0.8458 (t80) REVERT: J 72 GLN cc_start: 0.7388 (mt0) cc_final: 0.6863 (tm-30) REVERT: J 133 MET cc_start: 0.8539 (ptp) cc_final: 0.8234 (ptp) REVERT: J 154 TRP cc_start: 0.7645 (m-10) cc_final: 0.7328 (m-10) REVERT: J 280 MET cc_start: 0.7541 (tpt) cc_final: 0.7299 (tpt) REVERT: J 426 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8229 (mt) REVERT: M 43 ASP cc_start: 0.8513 (t0) cc_final: 0.8260 (t0) REVERT: M 61 ASP cc_start: 0.7910 (p0) cc_final: 0.7695 (p0) REVERT: M 133 ASN cc_start: 0.8658 (t0) cc_final: 0.7914 (t0) REVERT: M 153 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7405 (t0) REVERT: M 332 ARG cc_start: 0.7894 (ttp-170) cc_final: 0.6991 (ptm-80) REVERT: M 461 LEU cc_start: 0.6167 (tp) cc_final: 0.5893 (mp) REVERT: M 497 ARG cc_start: 0.7039 (tpp-160) cc_final: 0.5237 (tpp-160) REVERT: M 566 GLU cc_start: 0.4746 (mp0) cc_final: 0.3913 (tt0) REVERT: N 106 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7338 (mtp180) REVERT: N 133 MET cc_start: 0.8624 (mtt) cc_final: 0.8141 (mtt) REVERT: N 190 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7091 (ttt-90) REVERT: N 197 MET cc_start: 0.7523 (mmp) cc_final: 0.7234 (mmp) REVERT: N 270 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8009 (mmmm) REVERT: N 276 SER cc_start: 0.8568 (p) cc_final: 0.8343 (m) REVERT: N 302 LYS cc_start: 0.7947 (tttm) cc_final: 0.6894 (ttmm) outliers start: 213 outliers final: 117 residues processed: 672 average time/residue: 0.5812 time to fit residues: 642.8017 Evaluate side-chains 566 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 438 time to evaluate : 6.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 407 ILE Chi-restraints excluded: chain E residue 435 ILE Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 286 THR Chi-restraints excluded: chain I residue 319 ILE Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 276 SER Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 407 ILE Chi-restraints excluded: chain J residue 424 SER Chi-restraints excluded: chain J residue 426 LEU Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 153 ASP Chi-restraints excluded: chain M residue 157 LYS Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 189 PHE Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 386 GLU Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 106 ARG Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 253 THR Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 270 LYS Chi-restraints excluded: chain N residue 289 HIS Chi-restraints excluded: chain N residue 309 THR Chi-restraints excluded: chain N residue 329 ILE Chi-restraints excluded: chain N residue 337 SER Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 51 optimal weight: 0.9990 chunk 286 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 152 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 354 optimal weight: 0.9990 chunk 261 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 GLN ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 379 GLN ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN I 133 ASN ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 166 HIS ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 119 ASN ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.152447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.119888 restraints weight = 57703.837| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.67 r_work: 0.3443 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35670 Z= 0.182 Angle : 0.636 8.809 49080 Z= 0.323 Chirality : 0.042 0.344 5486 Planarity : 0.004 0.039 5684 Dihedral : 17.881 171.697 6512 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 5.99 % Allowed : 27.83 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3842 helix: 0.88 (0.14), residues: 1472 sheet: -0.68 (0.19), residues: 804 loop : -0.76 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP M 510 HIS 0.017 0.001 HIS M 52 PHE 0.022 0.002 PHE M 287 TYR 0.026 0.002 TYR N 291 ARG 0.007 0.000 ARG M 47 Details of bonding type rmsd hydrogen bonds : bond 0.04893 ( 1469) hydrogen bonds : angle 4.87321 ( 4142) covalent geometry : bond 0.00420 (35668) covalent geometry : angle 0.63565 (49080) Misc. bond : bond 0.00035 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 488 time to evaluate : 3.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 TRP cc_start: 0.8369 (m100) cc_final: 0.8019 (m100) REVERT: A 213 LEU cc_start: 0.8168 (mm) cc_final: 0.7747 (mm) REVERT: A 289 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8378 (tm-30) REVERT: A 318 SER cc_start: 0.8859 (OUTLIER) cc_final: 0.8613 (m) REVERT: B 34 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8047 (mp) REVERT: B 100 MET cc_start: 0.7276 (mmm) cc_final: 0.6774 (mmm) REVERT: E 16 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.7963 (p0) REVERT: E 93 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8367 (m-80) REVERT: E 234 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8132 (mpp) REVERT: E 492 ILE cc_start: 0.8995 (mt) cc_final: 0.8747 (mt) REVERT: E 572 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7332 (pt0) REVERT: F 249 ASP cc_start: 0.7661 (t0) cc_final: 0.7438 (t0) REVERT: F 256 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: I 206 ARG cc_start: 0.5930 (tpt90) cc_final: 0.5552 (ptt-90) REVERT: I 289 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7914 (tm-30) REVERT: I 306 ASP cc_start: 0.6899 (t0) cc_final: 0.6654 (t0) REVERT: I 397 ASN cc_start: 0.6153 (m-40) cc_final: 0.5879 (t0) REVERT: I 463 LYS cc_start: 0.8106 (tppt) cc_final: 0.7717 (tppt) REVERT: I 522 ASP cc_start: 0.8541 (m-30) cc_final: 0.8109 (t0) REVERT: I 547 LEU cc_start: 0.8225 (mm) cc_final: 0.7975 (mm) REVERT: J 40 TYR cc_start: 0.8709 (t80) cc_final: 0.8497 (t80) REVERT: J 72 GLN cc_start: 0.7318 (mt0) cc_final: 0.6925 (tm-30) REVERT: J 133 MET cc_start: 0.8603 (ptp) cc_final: 0.8268 (ptp) REVERT: J 154 TRP cc_start: 0.7590 (m-10) cc_final: 0.7351 (m-10) REVERT: M 131 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8203 (tm-30) REVERT: M 133 ASN cc_start: 0.8647 (t0) cc_final: 0.7692 (t0) REVERT: M 155 SER cc_start: 0.8389 (m) cc_final: 0.7946 (p) REVERT: M 332 ARG cc_start: 0.7910 (ttp-170) cc_final: 0.7253 (ptm-80) REVERT: M 462 ARG cc_start: 0.4954 (mtp85) cc_final: 0.4474 (mpt-90) REVERT: M 497 ARG cc_start: 0.6972 (tpp-160) cc_final: 0.4414 (tpp-160) REVERT: M 508 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7015 (pm20) REVERT: M 510 TRP cc_start: 0.7656 (t-100) cc_final: 0.7436 (t-100) REVERT: M 525 ARG cc_start: 0.7652 (ttp-170) cc_final: 0.7312 (ttp80) REVERT: M 566 GLU cc_start: 0.4895 (mp0) cc_final: 0.4083 (tt0) REVERT: M 579 PHE cc_start: 0.7209 (p90) cc_final: 0.6682 (p90) REVERT: N 49 GLN cc_start: 0.7899 (pm20) cc_final: 0.7637 (pm20) REVERT: N 190 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.6904 (ttt-90) REVERT: N 276 SER cc_start: 0.8670 (p) cc_final: 0.8361 (m) REVERT: N 302 LYS cc_start: 0.8020 (tttm) cc_final: 0.7607 (mtpp) outliers start: 200 outliers final: 124 residues processed: 641 average time/residue: 0.4765 time to fit residues: 497.6593 Evaluate side-chains 567 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 433 time to evaluate : 4.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 435 ILE Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 106 ARG Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 286 THR Chi-restraints excluded: chain I residue 318 SER Chi-restraints excluded: chain I residue 319 ILE Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 378 VAL Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 561 CYS Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 139 GLN Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 276 SER Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 345 VAL Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 424 SER Chi-restraints excluded: chain J residue 466 ILE Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 157 LYS Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 189 PHE Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 398 SER Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 253 THR Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 289 HIS Chi-restraints excluded: chain N residue 309 THR Chi-restraints excluded: chain N residue 337 SER Chi-restraints excluded: chain N residue 397 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 135 optimal weight: 7.9990 chunk 304 optimal weight: 0.0050 chunk 250 optimal weight: 3.9990 chunk 342 optimal weight: 0.0670 chunk 53 optimal weight: 0.0070 chunk 284 optimal weight: 8.9990 chunk 278 optimal weight: 0.5980 chunk 297 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 26 optimal weight: 0.0970 chunk 327 optimal weight: 10.0000 overall best weight: 0.1548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 GLN B 387 GLN E 16 ASN ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 HIS F 238 GLN ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 ASN I 16 ASN ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 195 ASN ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN M 52 HIS ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 139 GLN N 177 ASN ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 389 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.157284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.124286 restraints weight = 57274.432| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.71 r_work: 0.3524 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35670 Z= 0.115 Angle : 0.590 9.321 49080 Z= 0.299 Chirality : 0.040 0.236 5486 Planarity : 0.004 0.044 5684 Dihedral : 17.687 170.846 6501 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.94 % Allowed : 29.18 % Favored : 65.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3842 helix: 1.09 (0.14), residues: 1490 sheet: -0.46 (0.19), residues: 800 loop : -0.69 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 510 HIS 0.013 0.001 HIS M 52 PHE 0.021 0.001 PHE E 287 TYR 0.027 0.001 TYR I 162 ARG 0.006 0.000 ARG N 363 Details of bonding type rmsd hydrogen bonds : bond 0.04496 ( 1469) hydrogen bonds : angle 4.63967 ( 4142) covalent geometry : bond 0.00251 (35668) covalent geometry : angle 0.59031 (49080) Misc. bond : bond 0.00019 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 508 time to evaluate : 3.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.8885 (OUTLIER) cc_final: 0.8250 (p90) REVERT: A 21 MET cc_start: 0.7376 (ttm) cc_final: 0.7144 (ttm) REVERT: A 22 TRP cc_start: 0.8214 (m100) cc_final: 0.7974 (m100) REVERT: A 213 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7784 (mm) REVERT: A 289 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8250 (tm-30) REVERT: A 318 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8539 (m) REVERT: A 567 PHE cc_start: 0.6412 (m-80) cc_final: 0.6203 (m-80) REVERT: B 79 GLU cc_start: 0.8487 (mt-10) cc_final: 0.7765 (mm-30) REVERT: B 100 MET cc_start: 0.7195 (mmm) cc_final: 0.6656 (mmm) REVERT: E 16 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7530 (p0) REVERT: E 93 PHE cc_start: 0.8954 (OUTLIER) cc_final: 0.8187 (m-80) REVERT: E 194 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8617 (mt) REVERT: E 210 LYS cc_start: 0.8288 (tppt) cc_final: 0.7874 (mtmm) REVERT: E 492 ILE cc_start: 0.8969 (mt) cc_final: 0.8693 (mt) REVERT: E 572 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7275 (pt0) REVERT: F 249 ASP cc_start: 0.7663 (t0) cc_final: 0.7400 (t0) REVERT: I 206 ARG cc_start: 0.5896 (tpt90) cc_final: 0.5601 (ptt-90) REVERT: I 374 TYR cc_start: 0.5591 (t80) cc_final: 0.5350 (t80) REVERT: I 397 ASN cc_start: 0.6262 (m-40) cc_final: 0.5924 (t0) REVERT: I 463 LYS cc_start: 0.8130 (tppt) cc_final: 0.7764 (tppt) REVERT: I 547 LEU cc_start: 0.8238 (mm) cc_final: 0.7976 (mm) REVERT: J 72 GLN cc_start: 0.7183 (mt0) cc_final: 0.6728 (tm-30) REVERT: J 100 MET cc_start: 0.6314 (ppp) cc_final: 0.6092 (ppp) REVERT: J 133 MET cc_start: 0.8600 (ptp) cc_final: 0.8237 (ptp) REVERT: J 192 CYS cc_start: 0.7040 (t) cc_final: 0.6719 (t) REVERT: J 214 LYS cc_start: 0.8625 (ttpt) cc_final: 0.8351 (ttpt) REVERT: M 131 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8140 (tt0) REVERT: M 133 ASN cc_start: 0.8555 (t0) cc_final: 0.7447 (t0) REVERT: M 332 ARG cc_start: 0.7810 (ttp-170) cc_final: 0.7264 (ptm-80) REVERT: M 462 ARG cc_start: 0.5008 (mtp85) cc_final: 0.4462 (mpt-90) REVERT: M 508 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7008 (pm20) REVERT: M 525 ARG cc_start: 0.7522 (ttp-170) cc_final: 0.7251 (ttp80) REVERT: M 566 GLU cc_start: 0.5027 (mp0) cc_final: 0.4337 (tt0) REVERT: N 40 TYR cc_start: 0.7533 (t80) cc_final: 0.7333 (t80) REVERT: N 49 GLN cc_start: 0.7775 (pm20) cc_final: 0.7549 (pm20) REVERT: N 197 MET cc_start: 0.6714 (mmp) cc_final: 0.6493 (mmp) REVERT: N 276 SER cc_start: 0.8626 (p) cc_final: 0.8301 (m) REVERT: N 301 ARG cc_start: 0.7895 (ptm-80) cc_final: 0.7298 (tpt90) REVERT: N 302 LYS cc_start: 0.7948 (tttm) cc_final: 0.7712 (mmmt) outliers start: 165 outliers final: 90 residues processed: 636 average time/residue: 0.6097 time to fit residues: 634.0664 Evaluate side-chains 548 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 449 time to evaluate : 5.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 PHE Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 463 VAL Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 378 VAL Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 561 CYS Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 139 GLN Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 189 PHE Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 337 SER Chi-restraints excluded: chain N residue 345 VAL Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 118 optimal weight: 0.8980 chunk 73 optimal weight: 0.0970 chunk 210 optimal weight: 0.9980 chunk 401 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 204 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 255 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 185 optimal weight: 7.9990 chunk 365 optimal weight: 1.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 365 GLN F 238 GLN ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN I 16 ASN I 437 HIS ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.154655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.121217 restraints weight = 57160.770| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.73 r_work: 0.3479 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35670 Z= 0.143 Angle : 0.597 8.810 49080 Z= 0.303 Chirality : 0.040 0.216 5486 Planarity : 0.004 0.047 5684 Dihedral : 17.593 171.334 6499 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 5.33 % Allowed : 28.91 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.14), residues: 3842 helix: 1.11 (0.14), residues: 1488 sheet: -0.45 (0.19), residues: 800 loop : -0.75 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP M 510 HIS 0.011 0.001 HIS E 163 PHE 0.020 0.001 PHE E 523 TYR 0.022 0.001 TYR J 40 ARG 0.008 0.000 ARG M 47 Details of bonding type rmsd hydrogen bonds : bond 0.04458 ( 1469) hydrogen bonds : angle 4.60857 ( 4142) covalent geometry : bond 0.00327 (35668) covalent geometry : angle 0.59720 (49080) Misc. bond : bond 0.00019 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 469 time to evaluate : 5.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.8945 (OUTLIER) cc_final: 0.8327 (p90) REVERT: A 136 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7654 (mptp) REVERT: A 213 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7775 (mm) REVERT: A 289 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8345 (tm-30) REVERT: A 318 SER cc_start: 0.8759 (OUTLIER) cc_final: 0.8493 (m) REVERT: A 319 ILE cc_start: 0.8414 (pt) cc_final: 0.8180 (pt) REVERT: A 518 GLU cc_start: 0.8730 (pm20) cc_final: 0.8267 (pm20) REVERT: A 570 GLU cc_start: 0.7813 (pm20) cc_final: 0.7515 (tm-30) REVERT: B 100 MET cc_start: 0.6769 (mmm) cc_final: 0.6352 (mmm) REVERT: B 215 LEU cc_start: 0.8647 (mt) cc_final: 0.8434 (mt) REVERT: B 302 LYS cc_start: 0.8929 (ttpt) cc_final: 0.8470 (ttmm) REVERT: E 93 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8275 (m-80) REVERT: E 194 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8622 (mt) REVERT: E 234 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.7941 (mpp) REVERT: E 492 ILE cc_start: 0.8975 (mt) cc_final: 0.8689 (mt) REVERT: E 572 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7230 (pt0) REVERT: F 40 TYR cc_start: 0.8935 (t80) cc_final: 0.8714 (t80) REVERT: F 106 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7629 (mtp180) REVERT: I 206 ARG cc_start: 0.5844 (tpt90) cc_final: 0.5605 (ptt-90) REVERT: I 289 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7749 (tm-30) REVERT: I 310 ARG cc_start: 0.6867 (ptt-90) cc_final: 0.6465 (tpt-90) REVERT: I 397 ASN cc_start: 0.6209 (m-40) cc_final: 0.5889 (t0) REVERT: I 463 LYS cc_start: 0.8178 (tppt) cc_final: 0.7731 (tppt) REVERT: I 522 ASP cc_start: 0.8511 (m-30) cc_final: 0.8106 (t0) REVERT: I 547 LEU cc_start: 0.8297 (mm) cc_final: 0.8069 (mm) REVERT: J 49 GLN cc_start: 0.8276 (pm20) cc_final: 0.7882 (pt0) REVERT: J 72 GLN cc_start: 0.7183 (mt0) cc_final: 0.6746 (tm-30) REVERT: J 100 MET cc_start: 0.6256 (ppp) cc_final: 0.6053 (ppp) REVERT: J 133 MET cc_start: 0.8607 (ptp) cc_final: 0.8292 (ptp) REVERT: J 192 CYS cc_start: 0.7082 (t) cc_final: 0.6749 (t) REVERT: M 47 ARG cc_start: 0.8108 (mtt-85) cc_final: 0.7803 (mtt-85) REVERT: M 75 MET cc_start: 0.8976 (mmt) cc_final: 0.8774 (mmm) REVERT: M 133 ASN cc_start: 0.8663 (t0) cc_final: 0.7537 (t0) REVERT: M 332 ARG cc_start: 0.7794 (ttp-170) cc_final: 0.7028 (ptm-80) REVERT: M 462 ARG cc_start: 0.4982 (mtp85) cc_final: 0.4514 (mpt-90) REVERT: M 497 ARG cc_start: 0.6660 (tpp-160) cc_final: 0.3467 (tpp-160) REVERT: M 508 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6898 (pm20) REVERT: M 525 ARG cc_start: 0.7566 (ttp-170) cc_final: 0.7318 (ttp80) REVERT: M 579 PHE cc_start: 0.7266 (p90) cc_final: 0.6754 (p90) REVERT: N 76 THR cc_start: 0.8142 (OUTLIER) cc_final: 0.7857 (p) REVERT: N 276 SER cc_start: 0.8628 (p) cc_final: 0.8287 (m) REVERT: N 301 ARG cc_start: 0.7935 (ptm-80) cc_final: 0.7536 (tpt170) REVERT: N 302 LYS cc_start: 0.7978 (tttm) cc_final: 0.7756 (mmmt) outliers start: 178 outliers final: 124 residues processed: 607 average time/residue: 0.6480 time to fit residues: 648.0082 Evaluate side-chains 578 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 442 time to evaluate : 3.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 106 ARG Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 PHE Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 378 VAL Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 561 CYS Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 424 SER Chi-restraints excluded: chain J residue 466 ILE Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 189 PHE Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 329 ILE Chi-restraints excluded: chain N residue 330 GLU Chi-restraints excluded: chain N residue 337 SER Chi-restraints excluded: chain N residue 345 VAL Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 429 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 212 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 250 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 290 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 16 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 GLN ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN I 16 ASN ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 292 GLN ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.153016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.120791 restraints weight = 57382.026| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.52 r_work: 0.3473 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 35670 Z= 0.162 Angle : 0.604 9.062 49080 Z= 0.306 Chirality : 0.041 0.223 5486 Planarity : 0.004 0.049 5684 Dihedral : 17.574 171.033 6499 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.51 % Allowed : 28.85 % Favored : 65.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.14), residues: 3842 helix: 1.12 (0.14), residues: 1478 sheet: -0.46 (0.19), residues: 800 loop : -0.75 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP M 510 HIS 0.010 0.001 HIS E 163 PHE 0.021 0.001 PHE E 287 TYR 0.020 0.002 TYR N 229 ARG 0.007 0.000 ARG M 47 Details of bonding type rmsd hydrogen bonds : bond 0.04474 ( 1469) hydrogen bonds : angle 4.60872 ( 4142) covalent geometry : bond 0.00373 (35668) covalent geometry : angle 0.60404 (49080) Misc. bond : bond 0.00025 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 465 time to evaluate : 3.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.8947 (OUTLIER) cc_final: 0.8306 (p90) REVERT: A 22 TRP cc_start: 0.8364 (m100) cc_final: 0.7908 (m100) REVERT: A 209 HIS cc_start: 0.8132 (t-90) cc_final: 0.7922 (t-90) REVERT: A 213 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7834 (mm) REVERT: A 289 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8365 (tm-30) REVERT: A 318 SER cc_start: 0.8748 (OUTLIER) cc_final: 0.8487 (m) REVERT: A 319 ILE cc_start: 0.8479 (pt) cc_final: 0.8232 (pt) REVERT: A 518 GLU cc_start: 0.8728 (pm20) cc_final: 0.8300 (pm20) REVERT: A 567 PHE cc_start: 0.6265 (m-80) cc_final: 0.5940 (m-10) REVERT: A 570 GLU cc_start: 0.7874 (pm20) cc_final: 0.7505 (tm-30) REVERT: B 100 MET cc_start: 0.6828 (mmm) cc_final: 0.6408 (mmm) REVERT: E 16 ASN cc_start: 0.8220 (OUTLIER) cc_final: 0.7760 (p0) REVERT: E 93 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.8328 (m-80) REVERT: E 194 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8636 (mt) REVERT: E 234 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7867 (mpp) REVERT: E 244 ASN cc_start: 0.8625 (p0) cc_final: 0.8140 (t0) REVERT: E 492 ILE cc_start: 0.8983 (mt) cc_final: 0.8710 (mt) REVERT: E 572 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7259 (pt0) REVERT: F 106 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7678 (mtp180) REVERT: F 284 LEU cc_start: 0.9179 (mt) cc_final: 0.8897 (tp) REVERT: F 440 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.6889 (tttt) REVERT: I 206 ARG cc_start: 0.5921 (tpt90) cc_final: 0.5648 (ptt-90) REVERT: I 397 ASN cc_start: 0.6215 (m-40) cc_final: 0.5880 (t0) REVERT: I 437 HIS cc_start: 0.7288 (p90) cc_final: 0.7017 (p-80) REVERT: I 463 LYS cc_start: 0.8200 (tppt) cc_final: 0.7607 (tppt) REVERT: I 522 ASP cc_start: 0.8586 (m-30) cc_final: 0.8224 (t0) REVERT: I 547 LEU cc_start: 0.8451 (mm) cc_final: 0.8164 (mm) REVERT: I 556 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8369 (m) REVERT: J 49 GLN cc_start: 0.8279 (pm20) cc_final: 0.7865 (pt0) REVERT: J 72 GLN cc_start: 0.7228 (mt0) cc_final: 0.6774 (tm-30) REVERT: J 191 GLN cc_start: 0.7094 (mt0) cc_final: 0.6317 (pp30) REVERT: J 440 LYS cc_start: 0.8515 (mtpp) cc_final: 0.8198 (mtpp) REVERT: M 75 MET cc_start: 0.8976 (mmt) cc_final: 0.8747 (mmm) REVERT: M 133 ASN cc_start: 0.8734 (t0) cc_final: 0.7641 (t0) REVERT: M 332 ARG cc_start: 0.7863 (ttp-170) cc_final: 0.7518 (ptm-80) REVERT: M 381 LEU cc_start: 0.6682 (tp) cc_final: 0.6222 (tt) REVERT: M 462 ARG cc_start: 0.5139 (mtp85) cc_final: 0.4717 (mtt-85) REVERT: M 497 ARG cc_start: 0.6585 (tpp-160) cc_final: 0.3481 (tpp-160) REVERT: M 508 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7034 (pm20) REVERT: M 525 ARG cc_start: 0.7605 (ttp-170) cc_final: 0.7349 (ttp80) REVERT: N 25 ARG cc_start: 0.7554 (mtp85) cc_final: 0.7208 (mtt-85) REVERT: N 70 GLU cc_start: 0.7623 (tt0) cc_final: 0.7408 (tt0) REVERT: N 276 SER cc_start: 0.8641 (p) cc_final: 0.8319 (m) REVERT: N 301 ARG cc_start: 0.8051 (ptm-80) cc_final: 0.7368 (tpm170) REVERT: N 302 LYS cc_start: 0.8008 (tttm) cc_final: 0.7801 (mmmt) outliers start: 184 outliers final: 134 residues processed: 607 average time/residue: 0.4644 time to fit residues: 461.2517 Evaluate side-chains 584 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 437 time to evaluate : 3.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 407 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 106 ARG Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 440 LYS Chi-restraints excluded: chain F residue 463 VAL Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 378 VAL Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 556 THR Chi-restraints excluded: chain I residue 561 CYS Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 424 SER Chi-restraints excluded: chain J residue 466 ILE Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 189 PHE Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 309 THR Chi-restraints excluded: chain N residue 330 GLU Chi-restraints excluded: chain N residue 337 SER Chi-restraints excluded: chain N residue 345 VAL Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 413 SER Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 255 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 154 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 386 optimal weight: 10.0000 chunk 342 optimal weight: 0.0270 chunk 53 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 16 ASN A 120 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 ASN F 238 GLN ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN I 133 ASN ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 339 ASN ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.160649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.130336 restraints weight = 59153.083| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.47 r_work: 0.3664 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35670 Z= 0.125 Angle : 0.593 10.346 49080 Z= 0.299 Chirality : 0.040 0.249 5486 Planarity : 0.004 0.067 5684 Dihedral : 17.536 171.617 6497 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.73 % Allowed : 29.60 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3842 helix: 1.12 (0.14), residues: 1492 sheet: -0.39 (0.19), residues: 800 loop : -0.73 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP M 510 HIS 0.008 0.001 HIS E 163 PHE 0.022 0.001 PHE E 287 TYR 0.018 0.001 TYR J 40 ARG 0.011 0.000 ARG I 462 Details of bonding type rmsd hydrogen bonds : bond 0.04351 ( 1469) hydrogen bonds : angle 4.56209 ( 4142) covalent geometry : bond 0.00283 (35668) covalent geometry : angle 0.59274 (49080) Misc. bond : bond 0.00014 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 468 time to evaluate : 3.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASN cc_start: 0.9108 (OUTLIER) cc_final: 0.8904 (p0) REVERT: A 19 HIS cc_start: 0.8892 (OUTLIER) cc_final: 0.8375 (p90) REVERT: A 22 TRP cc_start: 0.8253 (m100) cc_final: 0.7856 (m100) REVERT: A 136 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7685 (mptp) REVERT: A 209 HIS cc_start: 0.8131 (t-90) cc_final: 0.7926 (t-90) REVERT: A 213 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7493 (mm) REVERT: A 289 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8358 (tm-30) REVERT: A 319 ILE cc_start: 0.8454 (pt) cc_final: 0.8209 (pt) REVERT: A 332 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8392 (mtp180) REVERT: A 518 GLU cc_start: 0.8618 (pm20) cc_final: 0.8316 (pm20) REVERT: A 567 PHE cc_start: 0.6356 (m-80) cc_final: 0.6018 (m-10) REVERT: B 100 MET cc_start: 0.6555 (mmm) cc_final: 0.6214 (mmm) REVERT: E 16 ASN cc_start: 0.8074 (OUTLIER) cc_final: 0.7848 (p0) REVERT: E 93 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8288 (m-80) REVERT: E 194 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8677 (mt) REVERT: E 244 ASN cc_start: 0.8543 (p0) cc_final: 0.8109 (t0) REVERT: E 492 ILE cc_start: 0.8966 (mt) cc_final: 0.8659 (mt) REVERT: E 572 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7237 (pt0) REVERT: F 106 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7503 (mtp180) REVERT: I 206 ARG cc_start: 0.5951 (tpt90) cc_final: 0.5743 (ptt-90) REVERT: I 310 ARG cc_start: 0.6874 (ptt-90) cc_final: 0.6514 (tpt-90) REVERT: I 397 ASN cc_start: 0.6283 (m-40) cc_final: 0.5917 (t0) REVERT: I 437 HIS cc_start: 0.7172 (p90) cc_final: 0.6564 (p-80) REVERT: I 463 LYS cc_start: 0.8197 (tppt) cc_final: 0.7674 (tppt) REVERT: I 522 ASP cc_start: 0.8541 (m-30) cc_final: 0.8210 (t0) REVERT: I 547 LEU cc_start: 0.8398 (mm) cc_final: 0.8165 (mm) REVERT: J 49 GLN cc_start: 0.8239 (pm20) cc_final: 0.7865 (pt0) REVERT: J 72 GLN cc_start: 0.7207 (mt0) cc_final: 0.6778 (tm-30) REVERT: J 133 MET cc_start: 0.8568 (ptp) cc_final: 0.8219 (ptp) REVERT: J 440 LYS cc_start: 0.8404 (mtpp) cc_final: 0.8152 (mtpp) REVERT: M 47 ARG cc_start: 0.8100 (mtt-85) cc_final: 0.7823 (mtt-85) REVERT: M 75 MET cc_start: 0.8989 (mmt) cc_final: 0.8735 (mmm) REVERT: M 133 ASN cc_start: 0.8493 (t0) cc_final: 0.7540 (t0) REVERT: M 244 ASN cc_start: 0.8552 (t0) cc_final: 0.8282 (p0) REVERT: M 332 ARG cc_start: 0.7983 (ttp-170) cc_final: 0.7506 (ptm-80) REVERT: M 381 LEU cc_start: 0.6755 (tp) cc_final: 0.6297 (tt) REVERT: M 403 TYR cc_start: 0.7168 (m-80) cc_final: 0.6913 (m-80) REVERT: M 497 ARG cc_start: 0.6567 (tpp-160) cc_final: 0.3589 (tpp-160) REVERT: M 508 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6963 (pm20) REVERT: M 525 ARG cc_start: 0.7554 (ttp-170) cc_final: 0.7301 (ttp80) REVERT: N 25 ARG cc_start: 0.7552 (mtp85) cc_final: 0.7071 (mtt-85) REVERT: N 197 MET cc_start: 0.7336 (mmp) cc_final: 0.6965 (mmp) REVERT: N 276 SER cc_start: 0.8664 (p) cc_final: 0.8288 (m) REVERT: N 301 ARG cc_start: 0.7983 (ptm-80) cc_final: 0.7626 (tpt90) outliers start: 158 outliers final: 117 residues processed: 594 average time/residue: 0.4679 time to fit residues: 450.4641 Evaluate side-chains 568 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 439 time to evaluate : 3.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 407 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 106 ARG Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 238 GLN Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 463 VAL Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 425 ILE Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 561 CYS Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 466 ILE Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 189 PHE Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 398 SER Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 309 THR Chi-restraints excluded: chain N residue 330 GLU Chi-restraints excluded: chain N residue 345 VAL Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 413 SER Chi-restraints excluded: chain N residue 429 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 95 optimal weight: 4.9990 chunk 234 optimal weight: 8.9990 chunk 351 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 391 optimal weight: 4.9990 chunk 230 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 241 optimal weight: 7.9990 chunk 352 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 15 GLN A 16 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 HIS ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 GLN F 295 HIS ** F 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 191 GLN ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.153407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.122493 restraints weight = 59528.652| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.55 r_work: 0.3548 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 35670 Z= 0.302 Angle : 0.729 11.027 49080 Z= 0.370 Chirality : 0.045 0.265 5486 Planarity : 0.005 0.052 5684 Dihedral : 17.678 171.833 6497 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.26 % Favored : 94.72 % Rotamer: Outliers : 5.78 % Allowed : 28.70 % Favored : 65.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.14), residues: 3842 helix: 0.72 (0.13), residues: 1480 sheet: -0.64 (0.19), residues: 784 loop : -0.90 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 510 HIS 0.012 0.001 HIS E 163 PHE 0.028 0.002 PHE E 287 TYR 0.027 0.002 TYR N 229 ARG 0.009 0.001 ARG M 47 Details of bonding type rmsd hydrogen bonds : bond 0.05027 ( 1469) hydrogen bonds : angle 4.87971 ( 4142) covalent geometry : bond 0.00692 (35668) covalent geometry : angle 0.72899 (49080) Misc. bond : bond 0.00109 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 431 time to evaluate : 3.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.9037 (OUTLIER) cc_final: 0.8475 (p90) REVERT: A 136 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7904 (mptp) REVERT: A 213 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7595 (mm) REVERT: A 289 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8423 (tm-30) REVERT: A 518 GLU cc_start: 0.8652 (pm20) cc_final: 0.8383 (pm20) REVERT: A 567 PHE cc_start: 0.6458 (m-80) cc_final: 0.6162 (m-10) REVERT: B 34 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8230 (mp) REVERT: B 100 MET cc_start: 0.6766 (mmm) cc_final: 0.6514 (mmm) REVERT: E 234 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7923 (mpp) REVERT: E 418 LYS cc_start: 0.8308 (tptm) cc_final: 0.7968 (tmtt) REVERT: E 492 ILE cc_start: 0.9036 (mt) cc_final: 0.8762 (mt) REVERT: E 572 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7376 (pt0) REVERT: F 290 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9111 (mp) REVERT: F 408 MET cc_start: 0.8982 (tpp) cc_final: 0.8766 (ttm) REVERT: I 206 ARG cc_start: 0.6038 (tpt90) cc_final: 0.5782 (ptt-90) REVERT: I 219 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8039 (p90) REVERT: I 397 ASN cc_start: 0.6252 (m-40) cc_final: 0.5820 (t0) REVERT: I 422 GLU cc_start: 0.7559 (pt0) cc_final: 0.6134 (tp30) REVERT: I 437 HIS cc_start: 0.7311 (p90) cc_final: 0.6714 (p-80) REVERT: I 547 LEU cc_start: 0.8445 (mm) cc_final: 0.8179 (mm) REVERT: J 72 GLN cc_start: 0.7323 (mt0) cc_final: 0.6836 (tm-30) REVERT: J 191 GLN cc_start: 0.7096 (mt0) cc_final: 0.6391 (pp30) REVERT: M 244 ASN cc_start: 0.8569 (t0) cc_final: 0.8278 (p0) REVERT: M 332 ARG cc_start: 0.8170 (ttp-170) cc_final: 0.7843 (ptm-80) REVERT: M 381 LEU cc_start: 0.6903 (tp) cc_final: 0.6378 (tt) REVERT: M 403 TYR cc_start: 0.7179 (m-80) cc_final: 0.6947 (m-80) REVERT: M 508 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7075 (pm20) REVERT: M 525 ARG cc_start: 0.7564 (ttp-170) cc_final: 0.7344 (ttp80) REVERT: N 76 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.8070 (p) REVERT: N 255 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.6017 (t80) REVERT: N 276 SER cc_start: 0.8773 (p) cc_final: 0.8286 (m) REVERT: N 301 ARG cc_start: 0.8251 (ptm-80) cc_final: 0.7686 (tpm170) outliers start: 193 outliers final: 143 residues processed: 581 average time/residue: 0.4682 time to fit residues: 446.1290 Evaluate side-chains 564 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 409 time to evaluate : 3.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 384 GLU Chi-restraints excluded: chain E residue 407 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 435 ILE Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 106 ARG Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 463 VAL Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 561 CYS Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 345 VAL Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 21 MET Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 189 PHE Chi-restraints excluded: chain M residue 234 MET Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 317 VAL Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 398 SER Chi-restraints excluded: chain M residue 409 GLN Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 289 HIS Chi-restraints excluded: chain N residue 309 THR Chi-restraints excluded: chain N residue 330 GLU Chi-restraints excluded: chain N residue 337 SER Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 413 SER Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 337 optimal weight: 3.9990 chunk 397 optimal weight: 0.8980 chunk 321 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 366 optimal weight: 1.9990 chunk 254 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 212 optimal weight: 0.8980 chunk 302 optimal weight: 2.9990 chunk 320 optimal weight: 0.5980 chunk 317 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 16 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 GLN ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 266 GLN N 141 HIS ** N 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.158587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.127356 restraints weight = 58910.595| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.56 r_work: 0.3623 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35670 Z= 0.142 Angle : 0.633 9.925 49080 Z= 0.321 Chirality : 0.041 0.278 5486 Planarity : 0.004 0.052 5684 Dihedral : 17.592 171.711 6495 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.93 % Favored : 96.04 % Rotamer: Outliers : 4.10 % Allowed : 30.56 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.14), residues: 3842 helix: 0.93 (0.14), residues: 1478 sheet: -0.51 (0.19), residues: 800 loop : -0.79 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP M 510 HIS 0.009 0.001 HIS B 104 PHE 0.024 0.002 PHE F 21 TYR 0.028 0.002 TYR N 84 ARG 0.011 0.000 ARG M 493 Details of bonding type rmsd hydrogen bonds : bond 0.04512 ( 1469) hydrogen bonds : angle 4.68282 ( 4142) covalent geometry : bond 0.00324 (35668) covalent geometry : angle 0.63294 (49080) Misc. bond : bond 0.00020 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 453 time to evaluate : 3.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.8923 (OUTLIER) cc_final: 0.8326 (p90) REVERT: A 22 TRP cc_start: 0.8371 (m100) cc_final: 0.7962 (m100) REVERT: A 136 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7759 (mptp) REVERT: A 213 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7484 (mm) REVERT: A 289 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8385 (tm-30) REVERT: A 332 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8529 (mtp180) REVERT: A 518 GLU cc_start: 0.8616 (pm20) cc_final: 0.8341 (pm20) REVERT: A 567 PHE cc_start: 0.6321 (m-80) cc_final: 0.6043 (m-10) REVERT: B 100 MET cc_start: 0.6681 (mmm) cc_final: 0.6401 (mmm) REVERT: B 299 MET cc_start: 0.7529 (mmm) cc_final: 0.7010 (mmm) REVERT: E 132 MET cc_start: 0.8751 (ttp) cc_final: 0.8367 (tmm) REVERT: E 244 ASN cc_start: 0.8577 (p0) cc_final: 0.8139 (t0) REVERT: E 492 ILE cc_start: 0.9006 (mt) cc_final: 0.8726 (mt) REVERT: E 572 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7318 (pt0) REVERT: F 106 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7648 (mtp180) REVERT: F 396 LYS cc_start: 0.7693 (tmtt) cc_final: 0.7467 (tmtt) REVERT: F 408 MET cc_start: 0.8979 (tpp) cc_final: 0.8764 (ttm) REVERT: I 397 ASN cc_start: 0.6206 (m-40) cc_final: 0.5873 (t0) REVERT: I 422 GLU cc_start: 0.7318 (pt0) cc_final: 0.5937 (tp30) REVERT: I 437 HIS cc_start: 0.7298 (p90) cc_final: 0.6720 (p-80) REVERT: I 463 LYS cc_start: 0.8204 (tppt) cc_final: 0.7730 (tppt) REVERT: I 522 ASP cc_start: 0.8638 (m-30) cc_final: 0.8281 (t0) REVERT: I 547 LEU cc_start: 0.8439 (mm) cc_final: 0.8171 (mm) REVERT: J 49 GLN cc_start: 0.8294 (pm20) cc_final: 0.7820 (pt0) REVERT: J 72 GLN cc_start: 0.7258 (mt0) cc_final: 0.6821 (tm-30) REVERT: J 133 MET cc_start: 0.8579 (ptp) cc_final: 0.8255 (ptp) REVERT: J 440 LYS cc_start: 0.8483 (mtpp) cc_final: 0.8194 (mtpp) REVERT: M 88 GLU cc_start: 0.6822 (tt0) cc_final: 0.6619 (tt0) REVERT: M 244 ASN cc_start: 0.8473 (t0) cc_final: 0.8245 (p0) REVERT: M 332 ARG cc_start: 0.8076 (ttp-170) cc_final: 0.7577 (ptm-80) REVERT: M 381 LEU cc_start: 0.6873 (tp) cc_final: 0.6404 (tt) REVERT: M 403 TYR cc_start: 0.7206 (m-80) cc_final: 0.6978 (m-80) REVERT: M 508 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6930 (pm20) REVERT: M 510 TRP cc_start: 0.7548 (t-100) cc_final: 0.7150 (t-100) REVERT: M 525 ARG cc_start: 0.7532 (ttp-170) cc_final: 0.7322 (ttp80) REVERT: N 76 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.8107 (p) REVERT: N 276 SER cc_start: 0.8719 (p) cc_final: 0.8300 (m) REVERT: N 301 ARG cc_start: 0.8214 (ptm-80) cc_final: 0.7606 (tpm170) outliers start: 137 outliers final: 113 residues processed: 565 average time/residue: 0.4751 time to fit residues: 439.6152 Evaluate side-chains 537 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 415 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 384 GLU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 106 ARG Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 463 VAL Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 405 ASP Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 561 CYS Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 345 VAL Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 424 SER Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 189 PHE Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 398 SER Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 330 GLU Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 413 SER Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 252 optimal weight: 7.9990 chunk 202 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 288 optimal weight: 0.5980 chunk 151 optimal weight: 0.2980 chunk 193 optimal weight: 4.9990 chunk 346 optimal weight: 8.9990 chunk 343 optimal weight: 1.9990 chunk 294 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 16 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 134 GLN ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 195 ASN ** N 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.158457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.128212 restraints weight = 58768.020| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.55 r_work: 0.3632 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35670 Z= 0.146 Angle : 0.632 10.639 49080 Z= 0.319 Chirality : 0.041 0.303 5486 Planarity : 0.004 0.051 5684 Dihedral : 17.547 171.555 6495 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.48 % Favored : 95.50 % Rotamer: Outliers : 3.95 % Allowed : 30.80 % Favored : 65.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3842 helix: 0.96 (0.14), residues: 1488 sheet: -0.52 (0.19), residues: 800 loop : -0.82 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP M 510 HIS 0.014 0.001 HIS N 60 PHE 0.021 0.001 PHE M 579 TYR 0.037 0.002 TYR N 84 ARG 0.012 0.000 ARG M 47 Details of bonding type rmsd hydrogen bonds : bond 0.04465 ( 1469) hydrogen bonds : angle 4.64454 ( 4142) covalent geometry : bond 0.00335 (35668) covalent geometry : angle 0.63195 (49080) Misc. bond : bond 0.00007 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 439 time to evaluate : 4.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.8949 (OUTLIER) cc_final: 0.8377 (p90) REVERT: A 22 TRP cc_start: 0.8263 (m100) cc_final: 0.7925 (m100) REVERT: A 136 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7734 (mptp) REVERT: A 213 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7522 (mm) REVERT: A 289 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8427 (tm-30) REVERT: A 332 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8539 (mtp180) REVERT: A 567 PHE cc_start: 0.6257 (m-80) cc_final: 0.6018 (m-10) REVERT: B 100 MET cc_start: 0.6628 (mmm) cc_final: 0.6340 (mmm) REVERT: B 280 MET cc_start: 0.8109 (tpp) cc_final: 0.7602 (tpp) REVERT: B 299 MET cc_start: 0.7418 (mmm) cc_final: 0.7089 (mmm) REVERT: E 94 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8175 (pt0) REVERT: E 244 ASN cc_start: 0.8570 (p0) cc_final: 0.8136 (t0) REVERT: E 418 LYS cc_start: 0.8069 (tptm) cc_final: 0.7867 (tmtt) REVERT: E 492 ILE cc_start: 0.9011 (mt) cc_final: 0.8720 (mt) REVERT: E 572 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7287 (pt0) REVERT: F 106 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7574 (mtp180) REVERT: F 396 LYS cc_start: 0.7695 (tmtt) cc_final: 0.7418 (tmtt) REVERT: I 397 ASN cc_start: 0.6138 (m-40) cc_final: 0.5771 (t0) REVERT: I 422 GLU cc_start: 0.7336 (pt0) cc_final: 0.5960 (tp30) REVERT: I 437 HIS cc_start: 0.7272 (p90) cc_final: 0.6741 (p-80) REVERT: I 463 LYS cc_start: 0.8233 (tppt) cc_final: 0.7649 (tppt) REVERT: I 547 LEU cc_start: 0.8437 (mm) cc_final: 0.8178 (mm) REVERT: J 72 GLN cc_start: 0.7252 (mt0) cc_final: 0.6867 (tm-30) REVERT: J 214 LYS cc_start: 0.8508 (ttmt) cc_final: 0.7887 (mtpt) REVERT: J 440 LYS cc_start: 0.8537 (mtpp) cc_final: 0.8282 (mtpp) REVERT: M 332 ARG cc_start: 0.8117 (ttp-170) cc_final: 0.7854 (ptm-80) REVERT: M 381 LEU cc_start: 0.6887 (tp) cc_final: 0.6393 (tt) REVERT: M 403 TYR cc_start: 0.7261 (m-80) cc_final: 0.7036 (m-80) REVERT: M 508 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7143 (pm20) REVERT: M 510 TRP cc_start: 0.7539 (t-100) cc_final: 0.7098 (t-100) REVERT: M 525 ARG cc_start: 0.7494 (ttp-170) cc_final: 0.7285 (ttp80) REVERT: N 76 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.8072 (p) REVERT: N 276 SER cc_start: 0.8691 (p) cc_final: 0.8269 (m) REVERT: N 301 ARG cc_start: 0.8279 (ptm-80) cc_final: 0.7466 (tpm170) outliers start: 132 outliers final: 108 residues processed: 550 average time/residue: 0.4772 time to fit residues: 433.0497 Evaluate side-chains 531 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 414 time to evaluate : 3.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 384 GLU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 106 ARG Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 463 VAL Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 405 ASP Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 561 CYS Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 345 VAL Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 189 PHE Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 317 VAL Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 398 SER Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 330 GLU Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 294 optimal weight: 10.0000 chunk 282 optimal weight: 6.9990 chunk 396 optimal weight: 3.9990 chunk 273 optimal weight: 7.9990 chunk 302 optimal weight: 4.9990 chunk 381 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 401 optimal weight: 6.9990 chunk 350 optimal weight: 4.9990 chunk 111 optimal weight: 0.2980 chunk 170 optimal weight: 1.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 ASN M 18 GLN M 134 GLN ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.158261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.127540 restraints weight = 59176.185| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.64 r_work: 0.3621 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.154 35670 Z= 0.205 Angle : 0.730 59.066 49080 Z= 0.389 Chirality : 0.043 0.576 5486 Planarity : 0.004 0.051 5684 Dihedral : 17.543 171.580 6491 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.53 % Favored : 95.45 % Rotamer: Outliers : 3.95 % Allowed : 30.83 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 3842 helix: 0.93 (0.14), residues: 1488 sheet: -0.52 (0.19), residues: 800 loop : -0.82 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP M 510 HIS 0.010 0.001 HIS N 60 PHE 0.022 0.001 PHE E 287 TYR 0.032 0.002 TYR N 84 ARG 0.012 0.000 ARG M 47 Details of bonding type rmsd hydrogen bonds : bond 0.04539 ( 1469) hydrogen bonds : angle 4.64777 ( 4142) covalent geometry : bond 0.00456 (35668) covalent geometry : angle 0.73048 (49080) Misc. bond : bond 0.00030 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20729.29 seconds wall clock time: 369 minutes 6.79 seconds (22146.79 seconds total)